Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?
On 11.06.2015 14:07, David McGiven wrote: Your 1-3% claim is based on the webpage you linked ? Is it reliable to compare GPU performances for gromacs with those of 3D videogames ? OK, you got me on this. As much as I'd wish I cannot really back up my claim of comparability. I have been out of office for one week but did some tests here for myself today. The system is Haswell/E (i7-5820K), GPU is single GTX-980 (the normal Gigabyte Model), the test run is ADH-cubic-vsites (reaction field) from the bottom of the Gromacs acceleration page (http://www.gromacs.org/GPU_acceleration). I can explicitly set the PCIe-x16 slots to 1.0, 2.0, and 3.0 (which I did). Theoretically (and practically), PCIe-x16 2.0 should be relatively close in bandwidth to PCIe-x8 3.0, so this should give some hints as what to expect. adh-cubic-vsites/rf - ns/day: PCIE-x16/1.0 54.46 PCIE-x16/2.0 61.81 PCIE-x16/3.0 64.52 percentage related to PCIE-x16/3.0 PCIE-x16/1.0 84.4 PCIE-x16/2.0 95.8 PCIE-x16/3.0 100 (each value = avg. of three runs) Therefore one could support the hypothesis that using one card in x16 and one in x8 would probably show a performance penalty of around 5% on the x8 card. Regards M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?
Good data Mirco, but let me emphasize that your measurements only reflect the case of heavily GPU-bound workloads! 5-6% performance improvement with PCI-E 3.0 vs 2.0 is about the maximum you'll see when, like in RF runs where, we there is no enough CPU work to fully overlap with the GPU computation (indicated by more than a few % in the Waif for GPU counter). However, if there is PME CPU work that balance well with the GPU work, while you will still get shorter CPU-GPU transfer times, the impact of this on the total runtime will be smaller. Cheers, -- Szilárd On Mon, Jun 15, 2015 at 4:10 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 11.06.2015 14:07, David McGiven wrote: Your 1-3% claim is based on the webpage you linked ? Is it reliable to compare GPU performances for gromacs with those of 3D videogames ? OK, you got me on this. As much as I'd wish I cannot really back up my claim of comparability. I have been out of office for one week but did some tests here for myself today. The system is Haswell/E (i7-5820K), GPU is single GTX-980 (the normal Gigabyte Model), the test run is ADH-cubic-vsites (reaction field) from the bottom of the Gromacs acceleration page (http://www.gromacs.org/GPU_acceleration). I can explicitly set the PCIe-x16 slots to 1.0, 2.0, and 3.0 (which I did). Theoretically (and practically), PCIe-x16 2.0 should be relatively close in bandwidth to PCIe-x8 3.0, so this should give some hints as what to expect. adh-cubic-vsites/rf - ns/day: PCIE-x16/1.0 54.46 PCIE-x16/2.0 61.81 PCIE-x16/3.0 64.52 percentage related to PCIE-x16/3.0 PCIE-x16/1.0 84.4 PCIE-x16/2.0 95.8 PCIE-x16/3.0 100 (each value = avg. of three runs) Therefore one could support the hypothesis that using one card in x16 and one in x8 would probably show a performance penalty of around 5% on the x8 card. Regards M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?
Dear Gromacs Users, We're finally buying some Intel E52650 servers + NVIDIA GTX980 cards. However, there's some servers that come with only PCI-e 3.0 x8 slots and others with x16 slots. Do you think this is relevant for gromacs performance ? And if so, how much relevant ? Thanks in advance. Cheers, David. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?
On 11.06.2015 13:08, David McGiven wrote: We're finally buying some Intel E52650 servers + NVIDIA GTX980 cards. However, there's some servers that come with only PCI-e 3.0 x8 slots and others with x16 slots. Do you think this is relevant for gromacs performance ? And if so, how much relevant ? It's more important to select PCIe 3.0 mode. Then, the difference between 16x and 8x is imho very low (1-3%). M. P.S.: http://www.techpowerup.com/reviews/NVIDIA/GTX_980_PCI-Express_Scaling/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?
Hey Mirco, Your 1-3% claim is based on the webpage you linked ? Is it reliable to compare GPU performances for gromacs with those of 3D videogames ? Thanks! 2015-06-11 13:21 GMT+02:00 Mirco Wahab mirco.wa...@chemie.tu-freiberg.de: On 11.06.2015 13:08, David McGiven wrote: We're finally buying some Intel E52650 servers + NVIDIA GTX980 cards. However, there's some servers that come with only PCI-e 3.0 x8 slots and others with x16 slots. Do you think this is relevant for gromacs performance ? And if so, how much relevant ? It's more important to select PCIe 3.0 mode. Then, the difference between 16x and 8x is imho very low (1-3%). M. P.S.: http://www.techpowerup.com/reviews/NVIDIA/GTX_980_PCI-Express_Scaling/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
